Re: [ccp4bb] should the final model be refined against full datset

Sorry, I don't quite understand your reasoning for how the structure is rendered useless if one refined it with all data. Would your argument also apply to all the structures that were refined before R-free existed? Quyen You should enter the statistics for the model and data that you ac

Re: [ccp4bb] should the final model be refined against full datset

2011 at 1:20 PM, Quyen Hoang wrote: Sorry, I don't quite understand your reasoning for how the structure is rendered useless if one refined it with all data. "Useless" was too strong a word (it's Friday, sorry). I guess simulated annealing can address the mode

Re: [ccp4bb] should the final model be refined against full datset

ithout doing SA first). Quyen On Oct 14, 2011, at 4:35 PM, Nat Echols wrote: On Fri, Oct 14, 2011 at 1:20 PM, Quyen Hoang mailto:qqho...@gmail.com>> wrote: Sorry, I don't quite understand your reasoning for how the structure is rendered useless if one refined it with all da

Re: [ccp4bb] what to do with disordered side chains

Quyen ___ Quyen Hoang, Ph.D Assistant Professor Department of Biochemistry and Molecular Biology, Stark Neurosciences Research Institute Indiana University School of Medicine 635 Barnhill Drive, Room MS0013D Indianapolis, Indiana 46202-5122 Phone: 317-274-4371 Fax: 317-274-4686 email:

Re: [ccp4bb] what to do with disordered side chains

We are getting off topic a little bit. Original topic: is it better to not build disordered sidechains or build them and let B-factors take care of it? Ed's poll got almost a 50:50 split. Question still unanswered. Second topic introduced by Pavel: "Your B-factors are valid within a harmoni

Re: [ccp4bb] what to do with disordered side chains

board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Quyen Hoang Sent: Thursday, March 31, 2011 3:55 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] what to do with disordered side chains We are getting off topic a little bit. Original topic: is it better to not build disordered sidechains or

Re: [ccp4bb] what to do with disordered side chains

hu, Mar 31, 2011 at 11:27:58AM -0400, Quyen Hoang wrote: >> Thank you for your post, Herman. >> Since there is no holy bible to provide guidance, perhaps we should hold >> off the idea of electing a "powerful dictator" to enforce this? >> - at least until we all can

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

Will this affect my reprocessing of the data with D*TREK on my journey to XPLORE the planets MERCURY and rPLUTO in my ENDEAVOUR to find and BUSTER some CRYSTALS with my on-board TNT into XPOWDER? I am still trying to GRASP the idea of AUTODOCKing on precise HKL locations based on the SHARP bu

Re: [ccp4bb] what to do with disordered side chains

If these users exist (I don't doubt that they do), then they would also might think that lysine residues sometimes look identical to alanine - if the atoms after beta carbon of the lysine are deleted in the PDB due to lack of density. So, I guess, if one's objectives in solving structures are to

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

d get all gitty Cheers, Quyen On Apr 4, 2011, at 5:19 AM, Eleanor Dodson wrote: Very clever.. Eleanor On 04/01/2011 03:19 PM, Quyen Hoang wrote: Will this affect my reprocessing of the data with D*TREK on my journey to XPLORE the planets MERCURY and rPLUTO in my ENDEAVOUR to find and BUSTER

Re: [ccp4bb] Nanodrop versus Nanophotomter Pearl versus good old Bradford.

We also have not experienced any problems with a Nanodrop 2000C. No one in my touched the two boxes of Bradford and BCA kits that we have, because we have been very happy with the Nanodrop. Quyen ___ Quyen Hoang, Ph.D Assistant Professor Department of Biochemistry

[ccp4bb] Postdoc Position in Molecular Neuroscience

interest in science and desire to learn new techniques to tackle challenging and important questions. Please email a cover letter, CV, and three reference letters to: qqho...@iupui.edu Thank you for looking and happy holidays! Cheers, Quyen ___ Quyen Hoang, Ph.D

Re: [ccp4bb] Reg. Protein purification

I have seen this when expressing sub-domains of a larger protein. Adding some (about 0.5% w/v) BOG (beta octylglucoside) worked well for cases similar to what you've described. Cheers, Quyen ___ Quyen Hoang, Ph.D Department of Biochemistry and Molecular Bi

Re: [ccp4bb] Deposition of riding H: R-factor is overrated

help to deposit two different models; one precisely reflects the model used in refinement and the other an energy minimized model with predicted hydrogens and alternative conformations removed? Cheers, Quyen ______ Quyen Hoang, Ph.D Assistant Professor Department

Re: [ccp4bb] Deposition of riding H: R-factor is overrated

way to resolve a significant problem that will likely to resurface down the road. It would be helpful if the more experienced people here can start a discussion of 'how to resolve' the problems exposed by this thread so far - assuming that you agree that it's a problem wort

[ccp4bb] Postdoctoral Position in Structure Biology of Neurodegenerative Disease

Postdoctoral position available: A postdoctoral position is available to study the mechanisms of Parkinson disease. Genetic studies in the past decade have identified a number of genes as causal factors of Parkinson disease. Our goals are to understand the biochemical and biological functio

Re: [ccp4bb] sulfur sad phasing

___ Quyen Hoang, Ph.D Department of Biochemistry and Molecular Biology, Start Neurosciences Research Institute Indiana University School of Medicine 635 Barnhill Drive, Room MS0013D Indianapolis, Indiana 46202-5122 Phone: 317-274-4371 Fax: 317-274-4686 email: qqho...@iupui.edu On Nov 11

Re: [ccp4bb] Optimisation of 2D very thin plates to thick plates

revealed that it was actually P21. Hope this helps. Cheers, Quyen Quyen Hoang, PhD Associate Professor of Biochemistry and Molecular Biology Adjunct Associate Professor of Neurology Primary Investigator of the Stark Neuroscience Research Institute Indiana University School of Medicine 635 Barnhill

[ccp4bb] Postdoctoral Positions Available

Postdoctoral Positions at Indiana University School of Medicine My lab will have two postdoc positions available, one immediately and the other in April 2015. A summary of what we do can be found at http://snri.iusm.iu.edu/people/primary-investigators/quyen-q-hoang-ph-d/

Re: [ccp4bb] Off topic - Mercury Lamp for Akta

We buy UV lamps from Jelight Company Inc. for replacements on our AKTA systems (http://www.jelight.com/low-pressure-uv-lamps.html ). It’s not a direct replacement in that a few modifications needed to be made: 1. cut two groves on the lamp base (

Re: [ccp4bb] vitrification vs freezing

I enjoyed following this thread. Because English is not my first language, I was hoping to learn the official definitions of these terms. In my opinion, all the variations proposed so far are fine - I don't see problems with using them. For me, when I see "flash frozen in liquid nitrogen" or "fl

Re: [ccp4bb] vitrification vs freezing

I was going to mention that too, but since I was a postdoc of Petsko my words could have been viewed as biased. Quyen On Nov 16, 2012, at 1:26 PM, Ronald E Stenkamp wrote: > I'm a little confused. Petsko and others were doing > low-temperature/freezing/vitrification crystal experiments in

Re: [ccp4bb] vitrification vs freezing

Hi Ed, > If we speak the way scientific articles are written... > > By Bernard Dixon, published in New Scientist, 11 April 1968, p.73, an > imaginary conversation at breakfast: > > "Daddy, I want cornflakes this morning. Must I have porridge?" > > "Yes. It has been suggested by mummy that, in

Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

I guess that one might need a way to avoid natural mutations that could turn B into B’ or B". Quyen Quyen Hoang, PhD Associate Professor of Biochemistry and Molecular Biology Adjunct Associate Professor of Neurology Primary Investigator of the Stark Neuroscience Research Institute In

[ccp4bb] Postdoc positions

...@iu.edu) if you are interested in learning more about these positions. Cheers, Quyen ___ Quyen Hoang, PhD Associate Professor of Biochemistry and Molecular Biology Director of IUSM Center for Electron Microscopy (iCEM) Adjunct Associate Professor of Neurology Primary Investigator of the Stark

[ccp4bb] Postdoctoral position in structural biology of neurodegeneration

ption of research interests and career goals, CV, and contact information for three references to Dr. Quyen Hoang (qqho...@iu.edu). Cheers, Quyen Quyen Hoang, PhD Associate Professor of Biochemistry and Molecular Biology Adjunct Associate Professor of Neurology Primary Investigator of the

Re: [ccp4bb] To Trim or Not to To Trim

no talk. Cheers, Quyen Quyen Hoang, PhD Professor of Biochemistry and Molecular Biology Director of IUSM Center for Electron Microscopy (iCEM) Adjunct Professor of Neurology Primary Investigator of the Stark Neuroscience Research Institute Indiana University School of Medicine 635

Re: [ccp4bb] To Trim or Not to To Trim

Hi Debanu,In your example, I would guess that models with truncated side chains would probably be problematic too, so would alternative conformations, unmodelled segments, asymmetric unit consisting of only a fraction of the biological/functional unit, etc.I am not sure if it is possible to build a

Re: [ccp4bb] [External] Re: [ccp4bb] Structure prediction - waiting to happen

Thank you for having this conversion. I have heard this question more than once (why is experimental determination needed when there is Alphafold) at grant study sections. Some came from structural biologists, so hopefully, the discussion here would help them also. Computational modeling had existe

[ccp4bb] Structure prediction - waiting to happen

time, I decided to learn how to solve the structure to proof > my prediction is correct. Now, it is interesting to see now the question is > on the other side. 😊 > > River > > From: CCP4 bulletin board <mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Quyen Hoan

[ccp4bb] Technician Position available

Hoang (qqho...@iu.edu). Cheers, Quyen __ Quyen Hoang, PhD Professor of Biochemistry and Molecular Biology Director of IUSM Center for Electron Microscopy (iCEM) Adjunct Professor of Neurology Primary Investigator of the Stark Neuroscience Research Institute Indiana University School of Medicin

Re: [ccp4bb] 3D/Stereoscopic hardware options in 2025?

Dear Wulf, I had the same problem. What I did was disconnect the computer from the university network - no longer part of its fleet, so no IT support. I'm glad to see there are other 3D fans. I, too, don’t understand how others do it without 3D. Cheers, Quyen __ Quyen Hoang, PhD Profess